The Chemistry of Life

1. Biology is a multidisciplinary science. • Living organisms are subject to basic laws of physics and chemistry. • One example is the bombardier beetle, which uses chemistry to defend itself. The Chemistry of Life

2. Atoms of elements play important roles in biology What element is lacking in her diet?

3. Atoms combine to make molecules The bonds between atoms of the same molecule are intramolecular bonds. The three types of intramolecular bonds are: • Covalent Bonds • Ionic Bonds • Polar Covalent Bonds

4. 1. Covalent Bonds The bond is formed by sharing a pair of valence electrons between two atoms. The bond can be represented in many ways. Name (molecular formula) Electron- shell diagram Space- filling model Structural formula Hydrogen (H2)

5. 2. Polar Covalent Bonds • This bond occurs when a pair of valence electrons is unequally shared between two atoms. • The atom with a larger nucleus attracts the electron more and has a slightly negative charge. • The other atom is slightly positive.

6. 3. Ionic Bond Formed by the transfer of an electron from atom to atom. This results in the formation of positive cations, and negative anions. Ions are held together by electrostatic attraction. Na Cl Na+ Cl– Sodium atom (an uncharged atom) Chlorine atom (an uncharged atom) Sodium ion (a cation) Chlorine ion (an anion) Sodium chloride (NaCl)

7. Pure Covalent Bonds Results from largely equal sharing of electrons. Happens when bond partners have similar electronegativities or an electronegativity difference of <0.5 Polar Covalent Bonds Results from unequal sharing of electrons. Happens when bond partners have electronegativity differences between 0.5 and 1.6 Properties of Covalent Bonds

8. The Role of Electronegativity Electronegativity is a measure of the strength with which an atom can attract electrons and can be found on a periodic table. The electronegativity difference between two atoms is calculated by subtracting the smaller value from the larger value.

9. Bond Types and Electronegativity • A difference of < 0. 5  covalent bond • A difference of 0.5 – 1.6  polar covalent bond • A difference of > 1.6  ionic bond

10. – O H H + + H2O Bonds in Water Oxygen electronegativity = 3.44 Hydrogen electronegativity = 2.2 Difference 3.44 – 2.2 = 1.24 Bond Type  Polar covalent In a water molecule the oxygen is slightly negatively charged.

11. Inter- Molecular Interactions The properties of molecules can influence their interactions with other molecules. These are weaker bonds than intramolecular bonds. • hydrogen bonding • dipole-dipole interactions • London/dispersion force

12. Water: A special molecule a) Hydrogen bonding Effects: cohesion, adhesion, surface tension. More energy is needed to break hydrogen bonds than other intermolecular bonds, which gives water a high specific heat capacity. b) Density Effects: Ice is less dense so it floats, insulating water underneath.

13. Water: A special molecule c) Polar nature of the bond Effects: as a solvent, water allows polar molecules and ionic compounds to dissolve due to water’s polarity d) Dissociation of intramolecular bonds Effects: 1 in 107 water molecules dissociates to form H+ and OH- ions. This is a pH of 7 = NEUTRAL.

14. Functional Groups • Functional groups are parts of larger molecules. • They greatly influence biological reactivity.

15. Functional Groups • Hydroxyl – alcohols • Carboxyl – acids • Amino – bases • Carbonyl – aldehydes and ketones

16. Functional Groups • One biologically important functional group missing from this list is sulfhydryl, which contains sulphur. The name of molecules with this functional group is thiol. The ‘R’ represents the rest of the molecule.

17. Functional Groups • Sulphur forms relatively strong intermolecular bonds with other sulphurs. This is important to forming the 3D structure of proteins.

18. Extra slides for students without chemistry background

19. STRUCTURE LE 4-10aa (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Alcohols (their specific names usually end in -ol) Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

20. Acetone, the simplest ketone EXAMPLE STRUCTURE LE 4-10ab Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

21. EXAMPLE STRUCTURE LE 4-10ac Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Has acidic properties because it is a source of hydrogen ions. Carboxylic acids, or organic acids The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

22. EXAMPLE STRUCTURE LE 4-10ba Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Acts as a base; can pick up a proton from the surrounding solution: Amine (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

23. EXAMPLE STRUCTURE LE 4-10bb (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Thiols

24. EXAMPLE STRUCTURE LE 4-10bc Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Organic phosphates Can transfer energy between organic molecules.